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pipeline:window:cryolo:picking
This version (2020/05/17 11:04) is a draft.
Approvals: 0/1
The Previously approved version (2019/09/14 10:14) is available.

Select the action “predict” and fill all arguments in the “Required arguments” tab:

Adjusting confidence threshold

In crYOLO, all particles have an assigned confidence value. By default, all particles with a confidence value below 0.3 are discarded. If you want to pick less or more conservatively you might want to change this confidence threshold to a less (e.g. 0.2) or more (e.g. 0.4) conservative value in the “Optional arguments” tab. However, it is much easier to select the best threshold after picking using the CBOX files written by crYOLO as described in the next section.

Monitor mode

When this option is activated, crYOLO will monitor your input folder. This especially useful for automation purposes. You can stop the monitor mode by writing an empty file with the name “stop.cryolo” in the input directory. Just add –monitor in the command line or check the monitor box in in the “Optional arguments” tab.

After picking is done, you can find four folders in your specified output folder:

• CBOX: Contains a coordinate file in .cbox format each input micrograph. It contains all detected particles, even those with a confidence lower the selected confidence threshold. Additionally it contains the confidence and the estimated diameter for each particle. Importing those files into the boxmanager allows you advanced filtering e.g. according size or confidence.
• EMAN: Contains a coordinate file in .box format each input micrograph. Only particles with the an confidence higher then the selected (default: 0.3) are contained in those files.
• STAR: Contains a coordinate file in .star format each input micrograph. Only particles with the an confidence higher then the selected (default: 0.3) are contained in those files.
• DISTR: Contains the plots of confidence- and size-distribution. Moroever, it contains a machine readable text-file the summary statistics about these distributions and their raw data in separate text-files.

► Press the the [Start] button to run the prediction.

Alternative: Run prediction from the command line

Click to display ⇲

Click to hide ⇱

To pick all your images in the directory full_data with the model weight file cryolo_model.h5 (e.g. or gmodel_phosnet_X_Y.h5 when using the general model) and and a confidence threshold of 0.3 run::

cryolo_predict.py -c config.json -w cryolo_model.h5 -i full_data/ -g 0 -o boxfiles/ -t 0.3

You will find the picked particles in the directory boxfiles.

pipeline/window/cryolo/picking.txt · Last modified: 2020/05/17 11:04 by twagner